Abstract Inhibition of the autolysosomal system has recently been described among the earliest changes in Alzheimer?s disease (AD) brains and likely contributes to the pathological hallmarks of AD: amyloid plaques and neurofibrillary Tau tangles that drive neurodegeneration. Impairment of the autolysosomal system and consequent disruption of molecular clearance are causally linked to increased neuronal vulnerability and neurodegeneration. Our recently published studies show that nuclear activity of the transcription factor EB (TFEB) and many cellular clearance mechanisms, are greatly attenuated in Presenilin (PS) deficiency, which is the leading cause for early onset familial AD (FAD). In our preliminary studies, we find that a decrease of nuclear calcium levels and consequently cAMP response element-binding protein (CREB)-mediated expression of its target genes associated with the autolysosomal pathway is the underlying mechanism for attenuated molecular clearance and decreased neuroprotection in PS and Tau mutants. Expression of the CREB-target gene sestrin 2 (sesn2) in human AD neurons promotes autophagic clearance and neuronal survival under stress conditions. We hypothesize that PS1 and Tau mutants impair Ryanodine Receptor (RyR)-mediated control of nuclear calcium, which promotes clearance of neurotoxic proteins that accumulate in the AD brain. If our hypothesis is correct, these studies will identify a novel pathway that drives formation of the pathological hallmarks associated with AD. Induced pluripotent stem cell (iPSC)-derived human forebrain neurons and Drosophila melanogaster will be used to assess the impact of nuclear calcium depletion and reduced pCREB signaling in molecular clearance during AD onset and progression. We seek to assess the relevance of our findings in postmortem human brain tissues from patients with early, mid and advanced AD. The use of complementary model systems allows us to assess causality: in human neurons that express physiological levels of disease-associated, aggregation-prone proteins, and in Drosophila melanogaster, a model organism with less complexity and redundancy than the human genome that can be genetically manipulated and physiologically aged. The overall goal of this proposal is 1) to understand the mechanisms leading to inhibition of molecular clearance in AD brains, and 2) to identify consequences of functional failure of neuronal clearance in aging and AD neurons to facilitate future development of interventions enhancing neuronal clearance and prevent neurodegeneration.